DNA–Protein Interaction Analysis (ChIP-Seq)

Abstract

ChIP-Seq, which combines chromatin immunoprecipitation (ChIP) with high throughput sequencing, is a powerful technology that allows for identification of genome-wide protein–DNA interactions. Interpretation of ChIP-Seq data has proven to be a complicated computational task, and multiple methods have been developed to address these challenges. This chapter begins by describing the protocol for ChIP-Seq library preparation and proper experimental design, without which computational tools would not be able to accurately capture in vivo interactions. Following a section on raw data pre-processing and data visualization, using Illumina Genome Analyzer output files as examples, general approaches taken by peak-calling tools are described. GLITR, a powerful peak-calling tool that utilizes a large set of control data to accurately identify regions that are bound in ChIP-Seq data, is then explained in detail. Finally, an approach for functional interpretation of ChIP-Seq peaks is discussed.